Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system.

Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3rd of that measured using the RTS 100 E. coli HY S30 system. Both of the 2 batch systems suffer from low ribosome recycling efficiency when translating proteins from 82 kD to 224 kD. A systematic fed-batch analysis of PURE shows replenishment of 6 small molecule substrates individually or in combination before energy depletion increased Fluc protein yield by ∼1.5 to ∼2-fold, while creatine phosphate and magnesium have synergistic effects when added to the PURE system. Additionally, while adding EF-P to PURE reduced full-length protein translated, it increased the fraction of functional protein and reduced partially translated protein probably by slowing down the translation process. Finally, ArfA, rather than YaeJ or PrfH, helped reduce ribosome stalling when translating Fluc and improved system productivity in a template-dependent fashion.

Optimization of scarless human stem cell genome editing.

Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows genetic modifications to be made more efficiently at targeted sites of interest. However, many opportunities remain to optimize these tools and to enlarge their spheres of application. We present several improvements: First, we developed functional re-coded TALEs (reTALEs), which not only enable simple one-pot TALE synthesis but also allow TALE-based applications to be performed using lentiviral vectors. We then compared genome-editing efficiencies in hiPSCs mediated by 15 pairs of reTALENs and Cas9-gRNA targeting CCR5 and optimized ssODN design in conjunction with both methods for introducing specific mutations. We found Cas9-gRNA achieved 7-8× higher non-homologous end joining efficiencies (3%) than reTALENs (0.4%) and moderately superior homology-directed repair efficiencies (1.0 versus 0.6%) when combined with ssODN donors in hiPSCs. Using the optimal design, we demonstrated a streamlined process to generated seamlessly genome corrected hiPSCs within 3 weeks.

Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis.

Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode for the entire translation machinery. Streamlined co-purification and reconstitution of the translation protein complex enabled protein synthesis in vitro. Our approach can be applied to a growing area of applications in in vitro one-pot multienzyme catalysis (MEC) to manipulate or enhance in vitro pathways such as natural product or carbohydrate biosynthesis.

A [2]rotaxane-based (1)H NMR spectroscopic probe for the simultaneous identification of physiologically important metal ions in solution.

We describe a [2]rotaxane molecule that exhibits distinct signals in its (1)H NMR spectra upon the complexation of physiologically important Li(+), Na(+), Mg(2+) and Ca(2+) ions; thus, the identification of these metal ions in solution is possible from the analysis of a single (1)H NMR spectrum of a single molecular sensor.

Is [N+-H...O] hydrogen bonding the most important noncovalent interaction in macrocycle-dibenzylammonium ion complexes?

We report a new host molecule in which one diethylene glycol chain (i.e., a loop possessing only three oxygen atoms) incorporated along with two phenolic aromatic rings is linked by a xylene spacer into a macroring. The design of the molecular structure of this macrocycle "amplifies" any potential [cation...pi], [N+-H...pi], and [N+C-H...pi] interactions between the dibenzylammonium (DBA+) ion and the phenolic rings of the macrocycle; as such, these species display a very strong binding affinity in CD3NO2 (Ka = 15,000 M(-1)). The macroring also coordinates to bipyridinium ions in a [2]pseudorotaxane fashion, which makes it the smallest macrocycle (i.e., a 25-membered ring) known to complex both DBA+ and bipyridinium ions in solution. To confirm unambiguously that these pseudorotaxanes exist in solution, we synthesized their corresponding interlocked molecules, namely rotaxanes and catenanes.